Monday, October 24, 2011
Try this at home by Daniel Grushkin
The next big scientific breakthrough may come from a garage, not a lab, with do-it-yourself biologists popping up everywhere. Genetic tinkerer Daniel Grushkin has a message for the curious: go ahead, try this at home.
In the scientific journals, we’ve been labeled biotech hobbyists, citizen scientists, even biohackers.Last December, seven of us opened the first community lab, called Genspace. Though it’s a fully functional lab, it has a decidedly hacked-together aesthetic. We built it in a Brooklyn, N.Y., warehouse that was converted into a workspace for architects and designers. At the center of the floor sits a glass cube made of found objects. The walls are created from windows and sliding glass doors saved from demo sites. The lab benches are stainless steel tables salvaged from industrial kitchens. Most of the equipment was donated by a biotech company that downsized during the economic crisis.We incorporated Genspace as a nonprofit to serve as a shared lab, a nursery for biotech tinkerers. Our members include an entrepreneur with great ideas but a miniscule budget, an artist employing single-celled organisms for an experimental design palette, a molecular biologist with a penchant for mentorship, and folks like me, who want to learn by creating novel organisms.
Wednesday, October 12, 2011
DIY Bio: Growing Movement takes On Aging
Article by H+ Magazine
A movement is growing quietly, steadily, and with great speed. In basements, attics, garages, and living rooms, amateurs and professionals alike are moving steadily towards disparate though unified goals. They come home from work or school and transform into biologists: do-it-yourself biologists, to be exact.
DIYbiology (“DIYbio”) is a homegrown synthesis of software, hardware, and wetware. In the tradition of homebrew computing and in the spirit of the Make space (best typified by o‘Reilly‘s Make Magazine), these DIYers hack much more than software and electronics. These biohackers build their own laboratory equipment, write their own code (computer and genetic) and design their own biological systems. They engineer tissue, purify proteins, extract nucleic acids and alter the genome itself. Whereas typical laboratory experiments can run from tens-of-thousands to millions of dollars, many DIYers knowledge of these fields is so complete that the best among them design and conduct their own experiments at stunningly low costs. With adequate knowledge and ingenuity, DIYbiologists can build equipment and run experiments on a hobbyist‘s budget. As the movement evolves, cooperatives are also springing up where hobbyists are pooling resources and creating “hacker spaces” and clubs to further reduce costs, share knowledge and boost morale.
A movement is growing quietly, steadily, and with great speed. In basements, attics, garages, and living rooms, amateurs and professionals alike are moving steadily towards disparate though unified goals. They come home from work or school and transform into biologists: do-it-yourself biologists, to be exact.
DIYbiology (“DIYbio”) is a homegrown synthesis of software, hardware, and wetware. In the tradition of homebrew computing and in the spirit of the Make space (best typified by o‘Reilly‘s Make Magazine), these DIYers hack much more than software and electronics. These biohackers build their own laboratory equipment, write their own code (computer and genetic) and design their own biological systems. They engineer tissue, purify proteins, extract nucleic acids and alter the genome itself. Whereas typical laboratory experiments can run from tens-of-thousands to millions of dollars, many DIYers knowledge of these fields is so complete that the best among them design and conduct their own experiments at stunningly low costs. With adequate knowledge and ingenuity, DIYbiologists can build equipment and run experiments on a hobbyist‘s budget. As the movement evolves, cooperatives are also springing up where hobbyists are pooling resources and creating “hacker spaces” and clubs to further reduce costs, share knowledge and boost morale.
The Pearl Gel Box and Creative Commons
Open Hardware for Molecular Biology Experiments
Sure it takes years of training to become a world class biologist, but now you can have fun with their equipment without slaving away in academia. Pearl Biotech is selling an electrophoresis gel box, an instrument used in the separation and characterization of DNA online. Electrophoresis is a safe procedure that is useful to molecular biologists but can be enjoyed by anyone. It’s a standard experiment in high school labs. The Pearl Gel Box is an open hardware device which means that anyone is free to build or adapt it as along as they share their modifications in a similar manner. Pearl Biotech sells a fully assembled version for $200. By providing a cheap entry level tool for genetics Pearl is helping generate interest in the field and supporting the do it yourself community.
Mammalian synthetic biology: engineering of sophisticated gene networks
J Biotechnol. 2007 Jul 15;130(4):329-45. Epub 2007 May 24.
(Must subscribe to see full text)
(Must subscribe to see full text)
Abstract:
With the recent development of a wide range of inducible mammalian transgene control systems it has now become possible to create functional synthetic gene networks by linking and connecting systems into various configurations. The past 5 years has thus seen the design and construction of the first synthetic mammalian gene regulatory networks. These networks have built upon pioneering advances in prokaryotic synthetic networks and possess an impressive range of functionalities that will some day enable the engineering of sophisticated inter- and intra-cellular functions to become a reality. At a relatively simple level, the modular linking of transcriptional components has enabled the creation of genetic networks that are strongly analogous to the architectural design and functionality of electronic circuits. Thus, by combining components in different serial or parallel configurations it is possible to produce networks that follow strict logic in integrating multiple independent signals (logic gates and transcriptional cascades) or which temporally modify input signals (time-delay circuits). Progressing in terms of sophistication, synthetic transcriptional networks have also been constructed which emulate naturally occurring genetic properties, such as bistability or dynamic instability. Toggle switches which possess "memory" so as to remember transient administered inputs, hysteric switches which are resistant to stochastic fluctuations in inputs, and oscillatory networks which produce regularly timed expression outputs, are all examples of networks that have been constructed using such properties. Initial steps have also been made in designing the above networks to respond not only to exogenous signals, but also endogenous signals that may be associated with aberrant cellular function or physiology thereby providing a means for tightly controlled gene therapy applications. Moving beyond pure transcriptional control, synthetic networks have also been created which utilize phenomena, such as post-transcriptional silencing, translational control, or inter-cellular signaling to produce novel network-based control both within and between cells. It is envisaged in the not-too-distant future that these networks will provide the basis for highly sophisticated genetic manipulations in biopharmaceutical manufacturing, gene therapy and tissue engineering applications.
With the recent development of a wide range of inducible mammalian transgene control systems it has now become possible to create functional synthetic gene networks by linking and connecting systems into various configurations. The past 5 years has thus seen the design and construction of the first synthetic mammalian gene regulatory networks. These networks have built upon pioneering advances in prokaryotic synthetic networks and possess an impressive range of functionalities that will some day enable the engineering of sophisticated inter- and intra-cellular functions to become a reality. At a relatively simple level, the modular linking of transcriptional components has enabled the creation of genetic networks that are strongly analogous to the architectural design and functionality of electronic circuits. Thus, by combining components in different serial or parallel configurations it is possible to produce networks that follow strict logic in integrating multiple independent signals (logic gates and transcriptional cascades) or which temporally modify input signals (time-delay circuits). Progressing in terms of sophistication, synthetic transcriptional networks have also been constructed which emulate naturally occurring genetic properties, such as bistability or dynamic instability. Toggle switches which possess "memory" so as to remember transient administered inputs, hysteric switches which are resistant to stochastic fluctuations in inputs, and oscillatory networks which produce regularly timed expression outputs, are all examples of networks that have been constructed using such properties. Initial steps have also been made in designing the above networks to respond not only to exogenous signals, but also endogenous signals that may be associated with aberrant cellular function or physiology thereby providing a means for tightly controlled gene therapy applications. Moving beyond pure transcriptional control, synthetic networks have also been created which utilize phenomena, such as post-transcriptional silencing, translational control, or inter-cellular signaling to produce novel network-based control both within and between cells. It is envisaged in the not-too-distant future that these networks will provide the basis for highly sophisticated genetic manipulations in biopharmaceutical manufacturing, gene therapy and tissue engineering applications.
Programmable cells: Interfacing natural and engineered gene networks
Article From Proceedings of the National Academy of Sciences of the United States of America.
(Full-text available)
Abstract:
Novel cellular behaviors and characteristics can be obtained by coupling engineered gene networks to the cell's natural regulatory circuitry through appropriately designed input and output interfaces. Here, we demonstrate how an engineered genetic circuit can be used to construct cells that respond to biological signals in a predetermined and programmable fashion. We employ a modular design strategy to create Escherichia coli strains where a genetic toggle switch is interfaced with: (i) the SOS signaling pathway responding to DNA damage, and (ii) a transgenic quorum sensing signaling pathway from Vibrio fischeri. The genetic toggle switch endows these strains with binary response dynamics and an epigenetic inheritance that supports a persistent phenotypic alteration in response to transient signals. These features are exploited to engineer cells that form biofilms in response to DNA-damaging agents and cells that activate protein synthesis when the cell population reaches a critical density. Our work represents a step toward the development of “plug-and-play” genetic circuitry that can be used to create cells with programmable behaviors.
Here is a fine discussion of the above article from an Openwetware blog.
(Full-text available)
Abstract:
Novel cellular behaviors and characteristics can be obtained by coupling engineered gene networks to the cell's natural regulatory circuitry through appropriately designed input and output interfaces. Here, we demonstrate how an engineered genetic circuit can be used to construct cells that respond to biological signals in a predetermined and programmable fashion. We employ a modular design strategy to create Escherichia coli strains where a genetic toggle switch is interfaced with: (i) the SOS signaling pathway responding to DNA damage, and (ii) a transgenic quorum sensing signaling pathway from Vibrio fischeri. The genetic toggle switch endows these strains with binary response dynamics and an epigenetic inheritance that supports a persistent phenotypic alteration in response to transient signals. These features are exploited to engineer cells that form biofilms in response to DNA-damaging agents and cells that activate protein synthesis when the cell population reaches a critical density. Our work represents a step toward the development of “plug-and-play” genetic circuitry that can be used to create cells with programmable behaviors.
Here is a fine discussion of the above article from an Openwetware blog.
Imaging brain electric signals with genetically targeted voltage-sensitive fluorescent proteins
(Must subscribe to view full article)
Cortical information processing relies on synaptic interactions between diverse classes of neurons with distinct electrophysiological and connection properties. Uncovering the operational principles of these elaborate circuits requires the probing of electrical activity from selected populations of defined neurons. Here we show that genetically encoded voltage-sensitive fluorescent proteins (VSFPs) provide an optical voltage report from targeted neurons in culture, acute brain slices and living mice. By expressing VSFPs in pyramidal cells of mouse somatosensory cortex, we also demonstrate that these probes can report cortical electrical responses to single sensory stimuli in vivo. These protein-based voltage probes will facilitate the analysis of cortical circuits in genetically defined cell populations and are hence a valuable addition to the optogenetic toolbox.
Clarifying brain structure, literally
A fluorescence-compatible tissue-clearing reagent enables light microscopy–based imaging deep in the mouse brain.
In The Invisible Man, a science fiction novella by Herbert G. Wells, the protagonist is a scientist who finds a way to make the human body invisible by changing its refractive index to prevent the bending and reflection of light. In a recent report, Atsushi Miyawaki and his colleagues at RIKEN described the development of a tissue-clearing reagent with similar effects, bridging the gap between science and fiction and enabling fluorescence-based imaging of biological tissues at unprecedented depth and subcellular resolution.
High-resolution microscopy methods and fluorescence-based labeling techniques have enabled the three-dimensional imaging and reconstruction of defined cellular populations in a variety of biological tissues. However, axial resolution and imaging depth are often limited by the intrinsic opacity of biological specimens. For example, in visualizing the mammalian brain, light microscopy–based advances have been confined to the few hundred micrometers under the organ's surface. Alternatively, mechanical sectioning or insertion of minuscule endoscopes can be used to access deeper structures, but such approaches are inevitably laborious, invasive or of limited perspective.
High-resolution microscopy methods and fluorescence-based labeling techniques have enabled the three-dimensional imaging and reconstruction of defined cellular populations in a variety of biological tissues. However, axial resolution and imaging depth are often limited by the intrinsic opacity of biological specimens. For example, in visualizing the mammalian brain, light microscopy–based advances have been confined to the few hundred micrometers under the organ's surface. Alternatively, mechanical sectioning or insertion of minuscule endoscopes can be used to access deeper structures, but such approaches are inevitably laborious, invasive or of limited perspective.
A GFP for RNA
Researchers describe a GFP mimic for fluorescently labeling RNA molecules.
The genetically encodable protein tag GFP and the rainbow of fluorescent variants it inspired have been indispensible for cell biology. Tagging RNAs in cells, however, is not so straightforward.
Samie Jaffrey's lab at Weill Medical College of Cornell University has long been interested in studying the role of RNAs in axon guidance. However, Jaffrey was frustrated that simple tools for visualizing RNAs were not available.
(This article relates to me, as well, because my senior seminar was on axon guidance, and I did not cover RNA mechanisms at all because I did not find any.)
The genetically encodable protein tag GFP and the rainbow of fluorescent variants it inspired have been indispensible for cell biology. Tagging RNAs in cells, however, is not so straightforward.
Samie Jaffrey's lab at Weill Medical College of Cornell University has long been interested in studying the role of RNAs in axon guidance. However, Jaffrey was frustrated that simple tools for visualizing RNAs were not available.
(This article relates to me, as well, because my senior seminar was on axon guidance, and I did not cover RNA mechanisms at all because I did not find any.)
Neuroscience Experiments
In the "Experiments" page of Backyard Brains are a series of nine increasingly complex experiments - from listening to action potentials to learning the basics of neuropharmacology and neuroprosthesis.
"Backyard Brains wiki page, [is] an open-source experimental how-to's for teachers and amateurs alike."
"Backyard Brains wiki page, [is] an open-source experimental how-to's for teachers and amateurs alike."
The page also lists the materials you will need to perform the experiments.
Tuesday, October 11, 2011
Synthetic biology: new engineering rules for an emerging discipline
From the Caltech Synthetic Biology Journal Club papers, I found this Nature Review:
Abstract
Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development.
Abstract
Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development.
Registry of Standard Biological Parts
The Registry is a continuously growing collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems. Founded in 2003 at MIT, the Registry is part of the Synthetic Biology community's efforts to make biology easier to engineer. It provides a resource of available genetic parts to iGEM teams and academic labs. You can register a new lab here.
The Registry sponsors international undergraduate teams (iGEM) to compete in building synthetic biology machines. This could be a good cause to make a group at university. It's another chance to boost a university's prestige and fame.
The Registry sponsors international undergraduate teams (iGEM) to compete in building synthetic biology machines. This could be a good cause to make a group at university. It's another chance to boost a university's prestige and fame.
Epigenetics
The development and maintenance of an organism is orchestrated by a set of chemical reactions that switch parts of the genome off and on at strategic times and locations. Epigenetics is the study of these reactions and the factors that influence them.
Making the Modern Do-It-Yourself Biology Laboratory (video)
Here is an article on the hardware, problems with wetware and DNA, and community labs as a solution to more efficient biohacking.
There was a time when only scientists used computers. Now systems that are thousands of times more powerful are available to nearly everyone. Bio-technology could follow the same course. However, if you want to tackle genetic testing, synthetic biology, etc then you’re going to need some serious hardware. Electrophoresis, polymerase chain reactions, fluorescent spectrometry – these are all really basic techniques but they still require specialized machines that can cost thousands of dollars. Luckily, that may be about to change. We’ve seen several projects to make cheap and even open hardware versions of lab devices – helping biotech become more do-it-yourself. While at the Open Source Summit I had the chance to talk with some of the forces behind these projects, as well as with the DIY enthusiasts that hope to one day use them. We may be approaching the age of the personal biology lab but there are some major hurdles still in the way.
It’s been more than a year since we covered DIYbio.org, the online website where many would be bio-tech hobbyists share information. DIYbio is just the most prominent face on a much larger trend – the growing interest among amateurs and citizen scientists to perform modern biology experiments. Whether you want to isolate some genes, engineer new form’s of brewer’s yeast, or track diseases, there may be a place for you in the DIY biology movement.
If you have a lab. Unlike amateur astronomy or amateur programming, amateur bio-technology needs a lot of equipment and supplies. To that end, certain members of the community have worked tirelessly to provide cheap, simple, and hackable versions of lab necessities. Once they become widely available these devices could also have an impact outside amateur science. What works for DIY hobbyists will help high school education, and could be leveraged for third world medicine as well.
It’s been more than a year since we covered DIYbio.org, the online website where many would be bio-tech hobbyists share information. DIYbio is just the most prominent face on a much larger trend – the growing interest among amateurs and citizen scientists to perform modern biology experiments. Whether you want to isolate some genes, engineer new form’s of brewer’s yeast, or track diseases, there may be a place for you in the DIY biology movement.
If you have a lab. Unlike amateur astronomy or amateur programming, amateur bio-technology needs a lot of equipment and supplies. To that end, certain members of the community have worked tirelessly to provide cheap, simple, and hackable versions of lab necessities. Once they become widely available these devices could also have an impact outside amateur science. What works for DIY hobbyists will help high school education, and could be leveraged for third world medicine as well.
Overview of DNA Sequencing Strategies
From: Current Protocols in Molecular Biology
ABSTRACT
Efficient and cost-effective DNA sequencing technologies have been, and may continue to be, critical to the progress of molecular biology. This overview of DNA sequencing strategies provides a high-level review of six distinct approaches to DNA sequencing: (a) dideoxy sequencing; (b) cyclic array sequencing; (c) sequencing-by-hybridization; (d) microelectrophoresis; (e) mass spectrometry; and (f) nanopore sequencing. The primary focus is on dideoxy sequencing, which has been the dominant technology since 1977, and on cyclic array strategies, for which several competitive implementations have been developed since 2005. Because the field of DNA sequencing is changing rapidly, this unit represents a snapshot of this particular moment
ABSTRACT
Efficient and cost-effective DNA sequencing technologies have been, and may continue to be, critical to the progress of molecular biology. This overview of DNA sequencing strategies provides a high-level review of six distinct approaches to DNA sequencing: (a) dideoxy sequencing; (b) cyclic array sequencing; (c) sequencing-by-hybridization; (d) microelectrophoresis; (e) mass spectrometry; and (f) nanopore sequencing. The primary focus is on dideoxy sequencing, which has been the dominant technology since 1977, and on cyclic array strategies, for which several competitive implementations have been developed since 2005. Because the field of DNA sequencing is changing rapidly, this unit represents a snapshot of this particular moment
RNA Synthetic Biology
From the SynBioChicago papers, I obtained this article.
Abstract:
RNA molecules play important and diverse regulatory roles in the cell by virtue of their interaction with other nucleic acids, proteins and small molecules. Inspired by this natural versatility, researchers have engineered RNA molecules with new biological functions. In the last two years efforts in synthetic biology have produced novel, synthetic RNA components capable of regulating gene expression in vivo largely in bacteria and yeast, setting the stage for scalable and programmable cellular behavior. Immediate challenges for this emerging field include determining how computational and directed-evolution techniques can be implemented to increase the complexity of engineered RNA systems, as well as determining how such systems can be broadly extended to
mammalian systems. Further challenges include designing RNA molecules to be sensors of intracellular and environmental stimuli, probes to explore the behavior of biological networks and components of engineered cellular control systems.
Abstract:
RNA molecules play important and diverse regulatory roles in the cell by virtue of their interaction with other nucleic acids, proteins and small molecules. Inspired by this natural versatility, researchers have engineered RNA molecules with new biological functions. In the last two years efforts in synthetic biology have produced novel, synthetic RNA components capable of regulating gene expression in vivo largely in bacteria and yeast, setting the stage for scalable and programmable cellular behavior. Immediate challenges for this emerging field include determining how computational and directed-evolution techniques can be implemented to increase the complexity of engineered RNA systems, as well as determining how such systems can be broadly extended to
mammalian systems. Further challenges include designing RNA molecules to be sensors of intracellular and environmental stimuli, probes to explore the behavior of biological networks and components of engineered cellular control systems.
My Smartphone Is A Microscope. What Can Yours Do?
From NPR:
I lied. My smartphone isn't a microscope — yet. But there are some smart physicists who want to make that transformation possible very soon, if not for you and me at first, then for doctors who don't have easy access to laboratories.
There are a lot of ways to trick out your smartphone. And if you're an eager Apple fan, the brand-new iPhone 4S will come with fancy apps that use its increasingly sophisticated camera to scan and image the world. A smartphone camera lens can measure objects, help translate words, and even tell you whether your potato chips have been caught in a food safety recall.
But Sebastian Wachsmann-Hogiu and colleagues at the Center for Biophotonics, Science and Technology at the University of California, Davis say a smartphone's camera lens can also serve as a microscope and a spectrometer, which both could be pretty handy for looking at blood samples.
A few years ago, Wachsmann-Hogiu was thinking about creating tools to help doctors do tests right at the site where they're caring for patients, something called "point-of-care testing."
He'd heard about bioengineer Daniel Fletcher's work developing a low-tech mobile microscope called CellScope. But Wachsmann-Hogiu was interested in making something even simpler. And he noticed that when water droplets formed on the top of his iPhone camera, they magnified the image. So he took a tiny lens — just 1 millimeter in diameter — and attached it to the phone to try to get a similar effect.
I lied. My smartphone isn't a microscope — yet. But there are some smart physicists who want to make that transformation possible very soon, if not for you and me at first, then for doctors who don't have easy access to laboratories.
There are a lot of ways to trick out your smartphone. And if you're an eager Apple fan, the brand-new iPhone 4S will come with fancy apps that use its increasingly sophisticated camera to scan and image the world. A smartphone camera lens can measure objects, help translate words, and even tell you whether your potato chips have been caught in a food safety recall.
But Sebastian Wachsmann-Hogiu and colleagues at the Center for Biophotonics, Science and Technology at the University of California, Davis say a smartphone's camera lens can also serve as a microscope and a spectrometer, which both could be pretty handy for looking at blood samples.
A few years ago, Wachsmann-Hogiu was thinking about creating tools to help doctors do tests right at the site where they're caring for patients, something called "point-of-care testing."
He'd heard about bioengineer Daniel Fletcher's work developing a low-tech mobile microscope called CellScope. But Wachsmann-Hogiu was interested in making something even simpler. And he noticed that when water droplets formed on the top of his iPhone camera, they magnified the image. So he took a tiny lens — just 1 millimeter in diameter — and attached it to the phone to try to get a similar effect.
The World of DIY Bio
From Genomeweb.com
In the past, we may have used "Do-It-Yourself Biology" to describe hobbies for people who liked nature. Perhaps that's still true, but a new group of enthusiasts has appeared on the scene. Raised on gel electrophoresis and high-school labs with GFP-cloning kits, this generation wants a more hands-on approach. They're not content with yesterday's pursuits like bird watching, ant farming, and germinating seeds in a glass dish. Nor are they strictly biologists; many DIYbio members, as they're known, are engineers and programmers, and they're determined to do biology in a new way and change the world.
In the past, we may have used "Do-It-Yourself Biology" to describe hobbies for people who liked nature. Perhaps that's still true, but a new group of enthusiasts has appeared on the scene. Raised on gel electrophoresis and high-school labs with GFP-cloning kits, this generation wants a more hands-on approach. They're not content with yesterday's pursuits like bird watching, ant farming, and germinating seeds in a glass dish. Nor are they strictly biologists; many DIYbio members, as they're known, are engineers and programmers, and they're determined to do biology in a new way and change the world.
DIYbio Guides
How to make Homebrew Bacterial Broth and Agar, including Lysogeny Brothand Luminescence Broth.
How to Isolate and Culture the bioluminescent bacterium Photobacterium phosphoreum, using luminescence broth from the above guide and a fresh unwashed squid from the market.
More at:
An Analysis of What #DIYbio Has and What It Needs
DIYbio and its more professionally oriented cousin, Garage Biotech, are undergoing a revolution at present. Essential equipment that used to cost thousands is now available at affordable prices, in many cases under open licensing schemes and open to community development. Knowledge of biology, genetics and the procedures underlying it all is being disseminated in ever-more-abstracted forms to make it easier to get started. And soon, even the biological components: strains, enzymes and substrates, will likely become mass-marketable.
It’s an exciting time to be involved in the development of tomorrow’s technology, and sometimes I find myself stepping back to consider what we have, and what we still need. I may as well share these musings with others to spare them the time, and perhaps to inspire someone with the know-how to fill in the gaps and help make this happen.
Wired On Biohacking
Genome at Home: Biohackers Build Their Own Labs
An engineer in this event, made his own Polymerase Chain Reaction (PCR) device and gel electrophoresis. He founded a company called CoFactor to try to sell a DIY genomics kit.
A tiny spare bedroom is not an ideal space for a high tech biofabrication facility. To get to the one Josh Perfetto is putting together, visitors must walk all the way to the back of his mostly unfurnished house in Saratoga, California—through the kitchen, past some empty rooms, across a den with a lone couch—then climb a poorly lit staircase and round a corner. The room itself is about 120 square feet and has one big window with a view of an adjacent roof. There’s an 8-foot-wide gap in the middle; the rest of the room is for science. “I thought about moving the lab to the empty living room downstairs,” Perfetto says. “I really need more space. But that’s right by the front door. I don’t want to freak people out.”
He laughs a little awkwardly, and it’s easy to see why he’s worried. With its Pyrex containers on metal racks and other clinical-looking equipment, the bedroom looks perfect for cooking crystal meth. A mass of wires spills out of a wooden box; on top sits a metal plate punched full of holes. A table holds several laptops, test tubes, a box of purple surgical gloves, a rack with pipettes in various sizes, rubber tubes connected to vials, an orange plastic box with a blue light in the bottom, and a centrifuge that looks like an oversize rice cooker. The wooden box is actually a homemade device for doing polymerase chain reactions (PCR), a process that turns small samples of DNA into quantities large enough to analyze. And the orange plastic thing runs gel electrophoresis, a way to sort DNA strands by size. Perfetto, an engineer, built a few of the gadgets himself.
“I’ve been sleeping in here,” says Mackenzie Cowell, Perfetto’s business partner. “And who knows what kinds of chemicals have soaked into this rug!” He flew out to California from Boston a week earlier and has been working with Perfetto on a DIY genomics kit to sell through their new business, CoFactor. The problem is, right now extracting and amplifying DNA at home still takes too many steps. The guys are worried that people won’t enjoy the process if it’s too complicated.
DIY Bio will not end the world
A skeptical view of DIY Bio. :
So I am pretty dubious of the notion that "organisms in the hands of amateurs could escape and cause outbreaks of incurable diseases or unpredictable environmental damage." There is no greater risk of that than there is of transgenic bacteria escaping from any of the thousands of molecular biology laboratories in our nation. Genetically modified yeast and E. coli are not considered serious biological hazards because the modified strains require special growing conditions -- including selection using antibiotics -- to maintain the modification. Otherwise they revert to just plain old yeast and E. coli.
Actually the more likely negative scenario is that these DIY labs will produce absolutely nothing. If you are a PhD researcher with a lot of practice, you could probably get this stuff to work. But these experiments often fail even with experienced researchers in controlled laboratory settings. The much more likely negative side is that many amateur researchers would have trouble getting their stuff to work and waste their money in the process.
It may be true, but nothing can replace the excitement of learning biology by actually doing it. Many people will be motivated to learn more, and try harder through their failed experiments. Even failures can teach us something!
Neuroscience for Everyone!
Backyard Brains
"Backyard Brains offers a series of exciting and affordable entry‐level Brain Recording Kits that provide the ability for students of all ages to learn about neurons.
For the first time ever, school children and amateur scientists will have access to similar tools used by neuroscientists worldwide to study Electrophysiology: the electrical activity ofneurons. By following a few simple steps, everyone can experience how the brain is able to communicate our senses, memories, hopes, and desires!"
"Backyard Brains offers a series of exciting and affordable entry‐level Brain Recording Kits that provide the ability for students of all ages to learn about neurons.
For the first time ever, school children and amateur scientists will have access to similar tools used by neuroscientists worldwide to study Electrophysiology: the electrical activity ofneurons. By following a few simple steps, everyone can experience how the brain is able to communicate our senses, memories, hopes, and desires!"
A synthetic multicellular system for programmed pattern formation
Letters to Nature
(Sorry, you have to pay to see the whole article, but the abstract is related to synthetic biology)
Garage biotech: Life hackers
Amateur hobbyists are creating home-brew molecular-biology labs, but can they ferment a revolution?
Rob Carlson's path to becoming a biohacker began with a chance encounter on the train in 1996. Carlson, a physics PhD student at the time, was travelling to New York to find a journal article that wasn't available at his home institution, Princeton University in New Jersey. He found himself sitting next to an inquisitive elderly gentlemen. Carlson told him about his thesis research on the effects of physical forces on blood cells, and at the end of the journey, the stranger made him an offer. "You should come work for me," said the man, "I'm Dr Sydney Brenner." The name meant little to Carlson, who says he thought: "Yeah, OK. Whatever, 'Dr Sydney Brenner.'"
It wasn't until Carlson got back to Princeton and asked a friend that he realized that "Dr Sydney Brenner" was a famed biologist with a knack for transforming the field. He took the job.
Within a year, Carlson was working with a motley crew of biologists, physicists and engineers at Brenner's Molecular Sciences Institute (MSI) in Berkeley, California, learning molecular biology techniques as he went along. The institute was a hotbed of creativity, and reminded Carlson of the scruffy hacker ethos that had spurred the personal-computing revolution just 25 years earlier. He began to wonder if the same thing could happen for biotechnology. What if a new industry, even a new culture, could be created by giving everyone access to the high-tech tools that he had at his fingertips? Most equipment was already for sale on websites such as eBay.
Carlson penned essays and articles that fanned the embers of the idea. "The era of garage biology is upon us," he wrote in a 2005 article in the technology magazine Wired. "Want to participate?" The democratization of science, he reasoned, would bring in new talent to build and improve scientific instrumentation, and maybe help to uncover new industrial applications for biotechnology. Eventually, he decided to follow his own advice, setting up a garage lab in 2005. "I made the prediction," he says, "so I figured maybe I should do the experiment."
Carlson is not alone. Would-be 'biohackers' around the world are setting up labs in their garages, closets and kitchens — from professional scientists keeping a side project at home to individuals who have never used a pipette before. They buy used lab equipment online, convert webcams into US$10 microscopes and incubate tubes of genetically engineered Escherichia coli in their armpits. (It's cheaper than shelling out $100 or more on a 37 °C incubator.) Some share protocols and ideas in open forums. Others prefer to keep their labs under wraps, concerned that authorities will take one look at the gear in their garages and label them as bioterrorists.
For now, most members of the do-it-yourself, or DIY, biology community are hobbyists, rigging up cheap equipment and tackling projects that — although not exactly pushing the boundaries of molecular biology — are creative proof of the hacker principle. Meredith Patterson, a computer programmer based in San Francisco, California, whom some call the 'doyenne of DIYbio', made glow-in-the-dark yogurt by engineering the bacteria within to produce a fluorescent protein. Others hope to learn more about themselves: a group called DIYgenomics has banded together to analyse their genomes, and even conduct and participate in small clinical trials. For those who aspire to change the world, improving biofuel development is a popular draw. And several groups are focused on making standard instruments — such as PCR machines, which amplify segments of DNA — cheaper and easier to use outside the confines of a laboratory, ultimately promising to make DIYbio more accessible.
Do-it-yourself biology grows with technology
New breed of scientists using technology to experiment outside usual lab settings
Here is a 2009 article from the San Francisco Gate on the stirrings of the embryonic DIY-Bio movement, and the safety concerns it raises. The movement started in 2008 at MIT with two students, but the strongest DIY-Bio today is in San Francisco.
Introduction
The aim of this blog is to be an account of a journey to understand biology, not for passing a scantron test, but for actually figuring out how nature works.
Yesterday, I first learned about a movement called DIY Bio (Do-It-Yourself Biology) by reading this article. It immediately appealed to me. Gregor Mendel's hobby contributed vastly to our knowledge of genetics, although he knew nothing about what a gene actually was. Santiago Ramon y Cajal was a painter, who turned his attention to the nervous system with the aid of accessible devices and his inventive methods. Charles Darwin sailed the world, and collected specimens before writing down his revolutionary ideas in the Origin of Species. However, I was always jealous of these scientists because they did not need a bachelor's degree, Ph.D., government grant, or corporate lab to contribute in a major way to science. Now, it seemed to me, all or most of these things were required.
With my personal discovery of DIY Bio, I hope I can actually do science here in Miami without having to wait to get an advanced degree. Of course, I am financially extremely limited, and am ignorant of the most powerful methods of study. However, I plan to overcome these obstacles in ways I have already planned.
I will post my progress and some articles on this blog. I welcome any feedback on tips, advice, and interest in the subject, too. All advancement in learning and understanding is a group effort. With this I begin...
Yesterday, I first learned about a movement called DIY Bio (Do-It-Yourself Biology) by reading this article. It immediately appealed to me. Gregor Mendel's hobby contributed vastly to our knowledge of genetics, although he knew nothing about what a gene actually was. Santiago Ramon y Cajal was a painter, who turned his attention to the nervous system with the aid of accessible devices and his inventive methods. Charles Darwin sailed the world, and collected specimens before writing down his revolutionary ideas in the Origin of Species. However, I was always jealous of these scientists because they did not need a bachelor's degree, Ph.D., government grant, or corporate lab to contribute in a major way to science. Now, it seemed to me, all or most of these things were required.
With my personal discovery of DIY Bio, I hope I can actually do science here in Miami without having to wait to get an advanced degree. Of course, I am financially extremely limited, and am ignorant of the most powerful methods of study. However, I plan to overcome these obstacles in ways I have already planned.
I will post my progress and some articles on this blog. I welcome any feedback on tips, advice, and interest in the subject, too. All advancement in learning and understanding is a group effort. With this I begin...
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